On November 1, 1897, the Republic of Biak-na-Bato was established in the cave of Biak-na-Bato, San Miguel de Mayumo, Bulacan. A special election was called for the new Supreme Council to oversee the newly established government on November 2, 1897 in the Philippines.

The convention aim to establish a revolutionary government to replace the Katipunan and settle the dispute between the two concils of Katipunan. Andres Bonifacio, the Supremo of the Katipunan, presided the over the election. He secured the unanimous pledge of the assembly to abide by the majority decision, However. Daniel Tirona contested and argued that a lawyer should handle the position for the Secretary of the Interior. Tirona recommended Jose del Rosario for the position. Bonifacio felt insulted and declared the convention null and void and leave the convention together with his supporters

Aguinaldo was elected in absentia. He was later notified by Col. Vicente Riego de Dios and told him that he won the election for the newly established government, Aguinaldo later left the battle to his brother Crisipulo to confirm the result of the election.

On December 14, 1897, the Pact of Biak-na-Bato was signed. Under the pact, Aguinaldo agreed to end hostilities and to exile himself and the revolutionary leadership, in exchange for amnesty and cash 'indemnities' in the amount of 800,000 pesos.[3] Aguinaldo took the money offered and, along with 34 other leaders of the rebellion, exiled himself in Hong Kong. The following were the officers of the Supreme Council that oversaw the pact. Emilio Aguinaldo was President and Mariano Trias, the Vice President. Other officials included Antonio Montenegro for Foreign Affairs, Isabelo Artacho for the Interior, Baldomero Aguinaldo for the Treasury, and Emiliano Riego de Dios for War.

However, thousands of other Katipuneros continued to fight the Revolution against Spain for a sovereign nation. Unlike Aguinaldo who came from a privileged background, the bulk of these fighters were peasants and workers who were not willing to settle for 'indemnities.'